From what I read, it was because of the sex, the nudity and some of the violence. i.e. his best friend hanging himself. So the military wanted no part of that.
All we have to decide is what to do with the time that is given to us. -Gandalf the Grey

What was wrong with An Officer and a Gentleman ? I'm sure there were technical errors but I don't really see the military being portrayed in a negative light.

The military rarely gets involved with the making of any films that portray them in either a negative or controversial light.
The military didn't want anything to do with An Officer and a Gentleman either.
"All we have to decide is what to do with the time that is given to us." -Gandalf the Grey

No, they did not have anything to do with making the picture.
In the rerelease of the book, at the begining the author talks about this very thing.
"I should point out here that the Department of Defense was not involved with this movie. Mace Neufeld has a good relationship with the DOD from his past films, but he felt that he should not seek government cooperation for this film. He said, "Over the years, I've worked with many wonderful people from the DOD who've played an invaluable role in certain projects, but I also know when the project is inappropiate and when to back off. It's a relationship if mutual respect.""